Multiple sequence alignment - TraesCS5B01G439800

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G439800 chr5B 100.000 2530 0 0 1 2530 611936133 611938662 0.000000e+00 4673
1 TraesCS5B01G439800 chr5B 96.140 1995 38 15 570 2530 641128789 641126800 0.000000e+00 3221
2 TraesCS5B01G439800 chr5B 90.000 210 16 1 373 577 611927561 611927770 1.490000e-67 267
3 TraesCS5B01G439800 chr5B 85.876 177 11 7 2 177 611927202 611927365 2.590000e-40 176
4 TraesCS5B01G439800 chr6A 96.472 1984 37 13 577 2530 617222870 617220890 0.000000e+00 3245
5 TraesCS5B01G439800 chr4A 96.330 1989 39 12 573 2530 36562908 36564893 0.000000e+00 3238
6 TraesCS5B01G439800 chr4A 95.754 2002 47 16 561 2530 690993546 690995541 0.000000e+00 3192
7 TraesCS5B01G439800 chr4B 96.416 1981 40 12 578 2530 578529982 578528005 0.000000e+00 3236
8 TraesCS5B01G439800 chr4B 95.913 1982 47 14 578 2530 91610229 91612205 0.000000e+00 3181
9 TraesCS5B01G439800 chr4B 95.770 1986 50 16 575 2530 407108834 407106853 0.000000e+00 3171
10 TraesCS5B01G439800 chr3B 96.324 1986 40 13 574 2530 812516877 812514896 0.000000e+00 3232
11 TraesCS5B01G439800 chr3B 96.345 1970 40 12 577 2517 379294092 379296058 0.000000e+00 3210
12 TraesCS5B01G439800 chr2B 96.187 1993 38 15 571 2530 776222953 776224940 0.000000e+00 3225
13 TraesCS5B01G439800 chr3A 96.268 1983 39 15 578 2530 54951918 54953895 0.000000e+00 3219
14 TraesCS5B01G439800 chr3A 96.065 1982 44 14 578 2530 736082942 736080966 0.000000e+00 3197
15 TraesCS5B01G439800 chr7B 96.167 1983 39 15 578 2530 202776916 202778891 0.000000e+00 3206
16 TraesCS5B01G439800 chr7B 95.921 1986 48 13 561 2517 692881436 692883417 0.000000e+00 3188
17 TraesCS5B01G439800 chr7B 95.637 1994 49 15 557 2517 552850575 552852563 0.000000e+00 3166
18 TraesCS5B01G439800 chr1B 96.030 1990 46 15 570 2530 7851069 7853054 0.000000e+00 3206
19 TraesCS5B01G439800 chrUn 96.016 1983 44 15 578 2530 175762113 175764090 0.000000e+00 3192
20 TraesCS5B01G439800 chr6B 97.476 634 11 2 574 1202 64173052 64173685 0.000000e+00 1077
21 TraesCS5B01G439800 chr5A 89.744 585 32 14 1 577 619449213 619449777 0.000000e+00 723
22 TraesCS5B01G439800 chr5D 85.311 177 12 7 2 177 495295797 495295960 1.200000e-38 171


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G439800 chr5B 611936133 611938662 2529 False 4673.0 4673 100.000 1 2530 1 chr5B.!!$F1 2529
1 TraesCS5B01G439800 chr5B 641126800 641128789 1989 True 3221.0 3221 96.140 570 2530 1 chr5B.!!$R1 1960
2 TraesCS5B01G439800 chr5B 611927202 611927770 568 False 221.5 267 87.938 2 577 2 chr5B.!!$F2 575
3 TraesCS5B01G439800 chr6A 617220890 617222870 1980 True 3245.0 3245 96.472 577 2530 1 chr6A.!!$R1 1953
4 TraesCS5B01G439800 chr4A 36562908 36564893 1985 False 3238.0 3238 96.330 573 2530 1 chr4A.!!$F1 1957
5 TraesCS5B01G439800 chr4A 690993546 690995541 1995 False 3192.0 3192 95.754 561 2530 1 chr4A.!!$F2 1969
6 TraesCS5B01G439800 chr4B 578528005 578529982 1977 True 3236.0 3236 96.416 578 2530 1 chr4B.!!$R2 1952
7 TraesCS5B01G439800 chr4B 91610229 91612205 1976 False 3181.0 3181 95.913 578 2530 1 chr4B.!!$F1 1952
8 TraesCS5B01G439800 chr4B 407106853 407108834 1981 True 3171.0 3171 95.770 575 2530 1 chr4B.!!$R1 1955
9 TraesCS5B01G439800 chr3B 812514896 812516877 1981 True 3232.0 3232 96.324 574 2530 1 chr3B.!!$R1 1956
10 TraesCS5B01G439800 chr3B 379294092 379296058 1966 False 3210.0 3210 96.345 577 2517 1 chr3B.!!$F1 1940
11 TraesCS5B01G439800 chr2B 776222953 776224940 1987 False 3225.0 3225 96.187 571 2530 1 chr2B.!!$F1 1959
12 TraesCS5B01G439800 chr3A 54951918 54953895 1977 False 3219.0 3219 96.268 578 2530 1 chr3A.!!$F1 1952
13 TraesCS5B01G439800 chr3A 736080966 736082942 1976 True 3197.0 3197 96.065 578 2530 1 chr3A.!!$R1 1952
14 TraesCS5B01G439800 chr7B 202776916 202778891 1975 False 3206.0 3206 96.167 578 2530 1 chr7B.!!$F1 1952
15 TraesCS5B01G439800 chr7B 692881436 692883417 1981 False 3188.0 3188 95.921 561 2517 1 chr7B.!!$F3 1956
16 TraesCS5B01G439800 chr7B 552850575 552852563 1988 False 3166.0 3166 95.637 557 2517 1 chr7B.!!$F2 1960
17 TraesCS5B01G439800 chr1B 7851069 7853054 1985 False 3206.0 3206 96.030 570 2530 1 chr1B.!!$F1 1960
18 TraesCS5B01G439800 chrUn 175762113 175764090 1977 False 3192.0 3192 96.016 578 2530 1 chrUn.!!$F1 1952
19 TraesCS5B01G439800 chr6B 64173052 64173685 633 False 1077.0 1077 97.476 574 1202 1 chr6B.!!$F1 628
20 TraesCS5B01G439800 chr5A 619449213 619449777 564 False 723.0 723 89.744 1 577 1 chr5A.!!$F1 576

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
406 410 0.099436 GCATGCGTCCTCATGAAACC 59.901 55.0 0.0 0.0 44.94 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2295 2525 1.061729 CTCACGCGTGTGCAAACAA 59.938 52.632 35.74 15.39 46.01 2.83 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.470664 TCACGTACAGTTAATTACCCCCAT 59.529 41.667 0.00 0.00 0.00 4.00
67 69 5.594317 GCTAGAATTTTCTTCCCATGCCTTA 59.406 40.000 0.00 0.00 38.70 2.69
69 71 7.448469 GCTAGAATTTTCTTCCCATGCCTTATA 59.552 37.037 0.00 0.00 38.70 0.98
185 187 6.033937 CGTTCATGTACCTCATCGCTAATATG 59.966 42.308 0.00 0.00 34.09 1.78
202 204 6.477033 GCTAATATGTGGAGTACAGTGACTTG 59.523 42.308 0.00 0.00 43.80 3.16
220 222 2.754946 TGTTTTGCGGGTAGGAGTAG 57.245 50.000 0.00 0.00 0.00 2.57
246 248 8.764524 AGTGACTTTGACATAGTAATGACTTC 57.235 34.615 0.00 0.00 37.10 3.01
247 249 7.542477 AGTGACTTTGACATAGTAATGACTTCG 59.458 37.037 0.00 0.00 37.10 3.79
260 262 5.613358 AATGACTTCGAATGTGAGGAAAC 57.387 39.130 0.00 0.00 0.00 2.78
284 288 5.636123 TGAGAATGAGAGAGAGGGGTATAC 58.364 45.833 0.00 0.00 0.00 1.47
286 290 2.273538 TGAGAGAGAGGGGTATACGC 57.726 55.000 11.34 11.34 0.00 4.42
290 294 1.819903 GAGAGAGGGGTATACGCATCC 59.180 57.143 25.30 18.18 39.90 3.51
375 379 1.846007 AAAAAGTGAGCACCCACACA 58.154 45.000 0.00 0.00 39.42 3.72
376 380 1.846007 AAAAGTGAGCACCCACACAA 58.154 45.000 0.00 0.00 39.42 3.33
377 381 1.846007 AAAGTGAGCACCCACACAAA 58.154 45.000 0.00 0.00 39.42 2.83
378 382 1.846007 AAGTGAGCACCCACACAAAA 58.154 45.000 0.00 0.00 39.42 2.44
379 383 1.102978 AGTGAGCACCCACACAAAAC 58.897 50.000 0.00 0.00 39.42 2.43
380 384 0.814457 GTGAGCACCCACACAAAACA 59.186 50.000 0.00 0.00 37.04 2.83
381 385 1.203523 GTGAGCACCCACACAAAACAA 59.796 47.619 0.00 0.00 37.04 2.83
382 386 1.476085 TGAGCACCCACACAAAACAAG 59.524 47.619 0.00 0.00 0.00 3.16
383 387 1.476488 GAGCACCCACACAAAACAAGT 59.524 47.619 0.00 0.00 0.00 3.16
384 388 1.204467 AGCACCCACACAAAACAAGTG 59.796 47.619 0.00 0.00 42.56 3.16
393 397 2.720578 CACAAAACAAGTGTAGCATGCG 59.279 45.455 13.01 0.00 32.44 4.73
394 398 2.357637 ACAAAACAAGTGTAGCATGCGT 59.642 40.909 13.01 3.35 0.00 5.24
395 399 2.969443 AAACAAGTGTAGCATGCGTC 57.031 45.000 13.01 10.03 0.00 5.19
396 400 1.156736 AACAAGTGTAGCATGCGTCC 58.843 50.000 13.01 4.66 0.00 4.79
397 401 0.321671 ACAAGTGTAGCATGCGTCCT 59.678 50.000 13.01 4.20 0.00 3.85
398 402 1.002366 CAAGTGTAGCATGCGTCCTC 58.998 55.000 13.01 5.24 0.00 3.71
399 403 0.608130 AAGTGTAGCATGCGTCCTCA 59.392 50.000 13.01 5.69 0.00 3.86
400 404 0.826715 AGTGTAGCATGCGTCCTCAT 59.173 50.000 13.01 0.00 0.00 2.90
401 405 0.933097 GTGTAGCATGCGTCCTCATG 59.067 55.000 13.01 0.00 44.93 3.07
402 406 0.823460 TGTAGCATGCGTCCTCATGA 59.177 50.000 13.01 0.00 44.94 3.07
403 407 1.206849 TGTAGCATGCGTCCTCATGAA 59.793 47.619 13.01 0.00 44.94 2.57
404 408 2.279741 GTAGCATGCGTCCTCATGAAA 58.720 47.619 13.01 0.00 44.94 2.69
405 409 1.089920 AGCATGCGTCCTCATGAAAC 58.910 50.000 13.01 0.00 44.94 2.78
406 410 0.099436 GCATGCGTCCTCATGAAACC 59.901 55.000 0.00 0.00 44.94 3.27
407 411 1.452110 CATGCGTCCTCATGAAACCA 58.548 50.000 0.00 0.03 44.94 3.67
408 412 1.811965 CATGCGTCCTCATGAAACCAA 59.188 47.619 0.00 0.00 44.94 3.67
409 413 1.522668 TGCGTCCTCATGAAACCAAG 58.477 50.000 0.00 0.00 0.00 3.61
410 414 1.202758 TGCGTCCTCATGAAACCAAGT 60.203 47.619 0.00 0.00 0.00 3.16
411 415 1.880027 GCGTCCTCATGAAACCAAGTT 59.120 47.619 0.00 0.00 0.00 2.66
412 416 3.071479 GCGTCCTCATGAAACCAAGTTA 58.929 45.455 0.00 0.00 0.00 2.24
413 417 3.500680 GCGTCCTCATGAAACCAAGTTAA 59.499 43.478 0.00 0.00 0.00 2.01
414 418 4.156008 GCGTCCTCATGAAACCAAGTTAAT 59.844 41.667 0.00 0.00 0.00 1.40
415 419 5.631026 CGTCCTCATGAAACCAAGTTAATG 58.369 41.667 0.00 0.00 0.00 1.90
416 420 5.402398 GTCCTCATGAAACCAAGTTAATGC 58.598 41.667 0.00 0.00 0.00 3.56
417 421 5.048083 GTCCTCATGAAACCAAGTTAATGCA 60.048 40.000 0.00 0.00 0.00 3.96
418 422 5.716228 TCCTCATGAAACCAAGTTAATGCAT 59.284 36.000 0.00 0.00 0.00 3.96
419 423 6.889177 TCCTCATGAAACCAAGTTAATGCATA 59.111 34.615 0.00 0.00 0.00 3.14
420 424 7.395772 TCCTCATGAAACCAAGTTAATGCATAA 59.604 33.333 0.00 0.00 0.00 1.90
421 425 8.034215 CCTCATGAAACCAAGTTAATGCATAAA 58.966 33.333 0.00 0.00 0.00 1.40
422 426 9.421806 CTCATGAAACCAAGTTAATGCATAAAA 57.578 29.630 0.00 0.00 0.00 1.52
423 427 9.941325 TCATGAAACCAAGTTAATGCATAAAAT 57.059 25.926 0.00 0.00 0.00 1.82
426 430 9.421806 TGAAACCAAGTTAATGCATAAAATCTG 57.578 29.630 0.00 0.10 0.00 2.90
427 431 8.776376 AAACCAAGTTAATGCATAAAATCTGG 57.224 30.769 0.00 10.64 0.00 3.86
428 432 6.877236 ACCAAGTTAATGCATAAAATCTGGG 58.123 36.000 18.96 15.45 0.00 4.45
429 433 6.667414 ACCAAGTTAATGCATAAAATCTGGGA 59.333 34.615 18.96 0.00 0.00 4.37
430 434 6.980397 CCAAGTTAATGCATAAAATCTGGGAC 59.020 38.462 0.00 0.00 0.00 4.46
431 435 7.147846 CCAAGTTAATGCATAAAATCTGGGACT 60.148 37.037 0.00 0.00 0.00 3.85
432 436 7.961326 AGTTAATGCATAAAATCTGGGACTT 57.039 32.000 0.00 0.00 0.00 3.01
433 437 8.366359 AGTTAATGCATAAAATCTGGGACTTT 57.634 30.769 0.00 0.00 0.00 2.66
434 438 8.470002 AGTTAATGCATAAAATCTGGGACTTTC 58.530 33.333 0.00 0.00 0.00 2.62
435 439 8.470002 GTTAATGCATAAAATCTGGGACTTTCT 58.530 33.333 0.00 0.00 0.00 2.52
436 440 9.693739 TTAATGCATAAAATCTGGGACTTTCTA 57.306 29.630 0.00 0.00 0.00 2.10
437 441 8.773033 AATGCATAAAATCTGGGACTTTCTAT 57.227 30.769 0.00 0.00 0.00 1.98
438 442 7.572523 TGCATAAAATCTGGGACTTTCTATG 57.427 36.000 0.00 0.00 0.00 2.23
439 443 6.039717 TGCATAAAATCTGGGACTTTCTATGC 59.960 38.462 0.00 0.00 36.80 3.14
440 444 6.515696 GCATAAAATCTGGGACTTTCTATGCC 60.516 42.308 0.00 0.00 31.98 4.40
441 445 4.870021 AAATCTGGGACTTTCTATGCCT 57.130 40.909 0.00 0.00 0.00 4.75
442 446 4.870021 AATCTGGGACTTTCTATGCCTT 57.130 40.909 0.00 0.00 0.00 4.35
443 447 3.634397 TCTGGGACTTTCTATGCCTTG 57.366 47.619 0.00 0.00 0.00 3.61
444 448 3.181329 TCTGGGACTTTCTATGCCTTGA 58.819 45.455 0.00 0.00 0.00 3.02
445 449 3.055094 TCTGGGACTTTCTATGCCTTGAC 60.055 47.826 0.00 0.00 0.00 3.18
446 450 2.642311 TGGGACTTTCTATGCCTTGACA 59.358 45.455 0.00 0.00 0.00 3.58
447 451 3.274288 GGGACTTTCTATGCCTTGACAG 58.726 50.000 0.00 0.00 0.00 3.51
448 452 3.274288 GGACTTTCTATGCCTTGACAGG 58.726 50.000 0.00 0.00 44.28 4.00
449 453 3.055094 GGACTTTCTATGCCTTGACAGGA 60.055 47.826 0.00 0.00 44.19 3.86
450 454 4.187694 GACTTTCTATGCCTTGACAGGAG 58.812 47.826 0.00 0.00 44.19 3.69
451 455 3.840666 ACTTTCTATGCCTTGACAGGAGA 59.159 43.478 0.00 0.00 44.19 3.71
452 456 4.472833 ACTTTCTATGCCTTGACAGGAGAT 59.527 41.667 0.00 0.00 44.19 2.75
453 457 4.412796 TTCTATGCCTTGACAGGAGATG 57.587 45.455 0.00 0.00 44.19 2.90
454 458 2.702478 TCTATGCCTTGACAGGAGATGG 59.298 50.000 0.00 0.00 44.19 3.51
455 459 1.588239 ATGCCTTGACAGGAGATGGA 58.412 50.000 0.00 0.00 44.19 3.41
456 460 0.907486 TGCCTTGACAGGAGATGGAG 59.093 55.000 0.00 0.00 44.19 3.86
457 461 0.908198 GCCTTGACAGGAGATGGAGT 59.092 55.000 0.00 0.00 44.19 3.85
458 462 1.280421 GCCTTGACAGGAGATGGAGTT 59.720 52.381 0.00 0.00 44.19 3.01
459 463 2.679349 GCCTTGACAGGAGATGGAGTTC 60.679 54.545 0.00 0.00 44.19 3.01
460 464 2.568956 CCTTGACAGGAGATGGAGTTCA 59.431 50.000 0.00 0.00 44.19 3.18
461 465 3.594134 CTTGACAGGAGATGGAGTTCAC 58.406 50.000 0.00 0.00 0.00 3.18
462 466 2.608623 TGACAGGAGATGGAGTTCACA 58.391 47.619 0.00 0.00 0.00 3.58
463 467 2.300152 TGACAGGAGATGGAGTTCACAC 59.700 50.000 0.00 0.00 0.00 3.82
464 468 2.300152 GACAGGAGATGGAGTTCACACA 59.700 50.000 0.00 0.00 0.00 3.72
465 469 2.037772 ACAGGAGATGGAGTTCACACAC 59.962 50.000 0.00 0.00 0.00 3.82
466 470 2.037641 CAGGAGATGGAGTTCACACACA 59.962 50.000 0.00 0.00 0.00 3.72
467 471 2.705658 AGGAGATGGAGTTCACACACAA 59.294 45.455 0.00 0.00 0.00 3.33
468 472 3.328931 AGGAGATGGAGTTCACACACAAT 59.671 43.478 0.00 0.00 0.00 2.71
469 473 3.438087 GGAGATGGAGTTCACACACAATG 59.562 47.826 0.00 0.00 0.00 2.82
470 474 3.415212 AGATGGAGTTCACACACAATGG 58.585 45.455 0.00 0.00 0.00 3.16
471 475 1.979855 TGGAGTTCACACACAATGGG 58.020 50.000 0.00 0.00 0.00 4.00
472 476 1.492599 TGGAGTTCACACACAATGGGA 59.507 47.619 0.00 0.00 39.75 4.37
477 481 0.950836 TCACACACAATGGGAAAGCG 59.049 50.000 0.00 0.00 37.99 4.68
478 482 0.667993 CACACACAATGGGAAAGCGT 59.332 50.000 0.00 0.00 30.67 5.07
479 483 1.876799 CACACACAATGGGAAAGCGTA 59.123 47.619 0.00 0.00 30.67 4.42
480 484 2.292016 CACACACAATGGGAAAGCGTAA 59.708 45.455 0.00 0.00 30.67 3.18
481 485 2.292292 ACACACAATGGGAAAGCGTAAC 59.708 45.455 0.00 0.00 0.00 2.50
482 486 2.552315 CACACAATGGGAAAGCGTAACT 59.448 45.455 0.00 0.00 0.00 2.24
483 487 3.004315 CACACAATGGGAAAGCGTAACTT 59.996 43.478 0.00 0.00 41.70 2.66
484 488 3.252458 ACACAATGGGAAAGCGTAACTTC 59.748 43.478 0.00 0.00 37.75 3.01
485 489 3.252215 CACAATGGGAAAGCGTAACTTCA 59.748 43.478 0.00 0.00 37.75 3.02
486 490 3.502211 ACAATGGGAAAGCGTAACTTCAG 59.498 43.478 0.00 0.00 37.75 3.02
487 491 2.922740 TGGGAAAGCGTAACTTCAGT 57.077 45.000 0.00 0.00 37.75 3.41
488 492 4.546829 ATGGGAAAGCGTAACTTCAGTA 57.453 40.909 0.00 0.00 37.75 2.74
489 493 4.339872 TGGGAAAGCGTAACTTCAGTAA 57.660 40.909 0.00 0.00 37.75 2.24
490 494 4.060205 TGGGAAAGCGTAACTTCAGTAAC 58.940 43.478 0.00 0.00 37.75 2.50
491 495 3.434641 GGGAAAGCGTAACTTCAGTAACC 59.565 47.826 0.00 0.00 37.75 2.85
492 496 3.122445 GGAAAGCGTAACTTCAGTAACCG 59.878 47.826 0.00 0.00 37.75 4.44
493 497 3.648339 AAGCGTAACTTCAGTAACCGA 57.352 42.857 0.00 0.00 30.77 4.69
494 498 3.648339 AGCGTAACTTCAGTAACCGAA 57.352 42.857 0.00 0.00 0.00 4.30
495 499 3.311966 AGCGTAACTTCAGTAACCGAAC 58.688 45.455 0.00 0.00 0.00 3.95
496 500 3.052036 GCGTAACTTCAGTAACCGAACA 58.948 45.455 0.00 0.00 0.00 3.18
497 501 3.676646 GCGTAACTTCAGTAACCGAACAT 59.323 43.478 0.00 0.00 0.00 2.71
498 502 4.433805 GCGTAACTTCAGTAACCGAACATG 60.434 45.833 0.00 0.00 0.00 3.21
499 503 4.433805 CGTAACTTCAGTAACCGAACATGC 60.434 45.833 0.00 0.00 0.00 4.06
500 504 3.120321 ACTTCAGTAACCGAACATGCA 57.880 42.857 0.00 0.00 0.00 3.96
501 505 3.067106 ACTTCAGTAACCGAACATGCAG 58.933 45.455 0.00 0.00 0.00 4.41
502 506 2.831685 TCAGTAACCGAACATGCAGT 57.168 45.000 0.00 0.00 0.00 4.40
503 507 3.945981 TCAGTAACCGAACATGCAGTA 57.054 42.857 0.00 0.00 0.00 2.74
504 508 3.581755 TCAGTAACCGAACATGCAGTAC 58.418 45.455 0.00 0.00 0.00 2.73
505 509 3.006003 TCAGTAACCGAACATGCAGTACA 59.994 43.478 0.00 0.00 0.00 2.90
506 510 3.743911 CAGTAACCGAACATGCAGTACAA 59.256 43.478 0.00 0.00 0.00 2.41
507 511 4.212425 CAGTAACCGAACATGCAGTACAAA 59.788 41.667 0.00 0.00 0.00 2.83
508 512 5.001232 AGTAACCGAACATGCAGTACAAAT 58.999 37.500 0.00 0.00 0.00 2.32
509 513 6.091577 CAGTAACCGAACATGCAGTACAAATA 59.908 38.462 0.00 0.00 0.00 1.40
510 514 5.950758 AACCGAACATGCAGTACAAATAA 57.049 34.783 0.00 0.00 0.00 1.40
511 515 6.509418 AACCGAACATGCAGTACAAATAAT 57.491 33.333 0.00 0.00 0.00 1.28
512 516 6.509418 ACCGAACATGCAGTACAAATAATT 57.491 33.333 0.00 0.00 0.00 1.40
513 517 6.551736 ACCGAACATGCAGTACAAATAATTC 58.448 36.000 0.00 0.00 0.00 2.17
514 518 6.150307 ACCGAACATGCAGTACAAATAATTCA 59.850 34.615 0.00 0.00 0.00 2.57
515 519 7.026562 CCGAACATGCAGTACAAATAATTCAA 58.973 34.615 0.00 0.00 0.00 2.69
516 520 7.701924 CCGAACATGCAGTACAAATAATTCAAT 59.298 33.333 0.00 0.00 0.00 2.57
517 521 9.075519 CGAACATGCAGTACAAATAATTCAATT 57.924 29.630 0.00 0.00 0.00 2.32
523 527 9.518906 TGCAGTACAAATAATTCAATTATGCTG 57.481 29.630 3.28 7.06 35.71 4.41
524 528 8.971321 GCAGTACAAATAATTCAATTATGCTGG 58.029 33.333 3.28 0.00 35.71 4.85
525 529 8.971321 CAGTACAAATAATTCAATTATGCTGGC 58.029 33.333 3.28 3.46 35.71 4.85
526 530 8.694540 AGTACAAATAATTCAATTATGCTGGCA 58.305 29.630 3.28 0.00 35.71 4.92
527 531 8.971321 GTACAAATAATTCAATTATGCTGGCAG 58.029 33.333 10.94 10.94 35.71 4.85
528 532 6.987992 ACAAATAATTCAATTATGCTGGCAGG 59.012 34.615 17.64 0.00 35.71 4.85
529 533 6.736110 AATAATTCAATTATGCTGGCAGGT 57.264 33.333 17.64 0.00 35.71 4.00
530 534 4.395959 AATTCAATTATGCTGGCAGGTG 57.604 40.909 17.64 0.00 0.00 4.00
531 535 1.105457 TCAATTATGCTGGCAGGTGC 58.895 50.000 17.64 3.06 41.14 5.01
532 536 0.818938 CAATTATGCTGGCAGGTGCA 59.181 50.000 17.64 9.70 44.36 4.57
535 539 2.036731 ATGCTGGCAGGTGCATGT 59.963 55.556 17.64 0.00 46.58 3.21
536 540 2.348104 ATGCTGGCAGGTGCATGTG 61.348 57.895 17.64 0.00 46.58 3.21
537 541 4.430765 GCTGGCAGGTGCATGTGC 62.431 66.667 17.64 13.43 44.36 4.57
542 546 3.066190 CAGGTGCATGTGCCCTGG 61.066 66.667 23.55 12.32 46.46 4.45
543 547 4.371417 AGGTGCATGTGCCCTGGG 62.371 66.667 8.86 8.86 39.27 4.45
544 548 4.365111 GGTGCATGTGCCCTGGGA 62.365 66.667 19.27 0.00 41.18 4.37
545 549 2.283101 GTGCATGTGCCCTGGGAA 60.283 61.111 19.27 1.51 41.18 3.97
546 550 1.683365 GTGCATGTGCCCTGGGAAT 60.683 57.895 19.27 3.32 41.18 3.01
547 551 1.380246 TGCATGTGCCCTGGGAATC 60.380 57.895 19.27 6.10 41.18 2.52
548 552 1.380246 GCATGTGCCCTGGGAATCA 60.380 57.895 19.27 11.95 34.31 2.57
549 553 1.669999 GCATGTGCCCTGGGAATCAC 61.670 60.000 19.27 15.62 34.31 3.06
550 554 0.323633 CATGTGCCCTGGGAATCACA 60.324 55.000 21.80 21.80 42.66 3.58
551 555 0.632835 ATGTGCCCTGGGAATCACAT 59.367 50.000 23.70 23.70 43.08 3.21
552 556 1.294041 TGTGCCCTGGGAATCACATA 58.706 50.000 19.27 0.00 34.87 2.29
553 557 1.212688 TGTGCCCTGGGAATCACATAG 59.787 52.381 19.27 0.00 34.87 2.23
554 558 0.846015 TGCCCTGGGAATCACATAGG 59.154 55.000 19.27 0.00 0.00 2.57
555 559 0.846693 GCCCTGGGAATCACATAGGT 59.153 55.000 19.27 0.00 0.00 3.08
556 560 1.477558 GCCCTGGGAATCACATAGGTG 60.478 57.143 19.27 0.00 46.66 4.00
557 561 1.143684 CCCTGGGAATCACATAGGTGG 59.856 57.143 7.01 0.00 45.32 4.61
558 562 1.477558 CCTGGGAATCACATAGGTGGC 60.478 57.143 7.81 0.00 45.32 5.01
559 563 1.212688 CTGGGAATCACATAGGTGGCA 59.787 52.381 7.81 0.00 45.32 4.92
560 564 1.852309 TGGGAATCACATAGGTGGCAT 59.148 47.619 7.81 0.00 45.32 4.40
561 565 2.233271 GGGAATCACATAGGTGGCATG 58.767 52.381 7.81 0.00 45.32 4.06
562 566 2.423373 GGGAATCACATAGGTGGCATGT 60.423 50.000 7.81 0.00 45.32 3.21
563 567 3.181445 GGGAATCACATAGGTGGCATGTA 60.181 47.826 7.81 0.00 45.32 2.29
564 568 4.507335 GGGAATCACATAGGTGGCATGTAT 60.507 45.833 7.81 0.00 45.32 2.29
565 569 4.456911 GGAATCACATAGGTGGCATGTATG 59.543 45.833 7.81 14.28 45.32 2.39
625 629 2.358898 GTGTCCATGTGCTCAGTTTTGT 59.641 45.455 0.00 0.00 0.00 2.83
802 811 1.131638 TGTGAGACCCAGCAAAGAGT 58.868 50.000 0.00 0.00 0.00 3.24
1175 1221 1.772453 GAATGGGGTAAGAATCGGGGA 59.228 52.381 0.00 0.00 0.00 4.81
1202 1390 1.477700 ACCATTTTCGTCGTCGGGATA 59.522 47.619 1.55 0.00 37.69 2.59
1301 1509 4.660168 AGAAGAGCATGAAGAATGGTTGT 58.340 39.130 0.00 0.00 46.95 3.32
1408 1616 6.874288 GCTATTGAGCTTAGGATGTTGAAT 57.126 37.500 0.00 0.00 45.98 2.57
1727 1935 0.035881 CTGCTCTGCCTTTCTGTCCA 59.964 55.000 0.00 0.00 0.00 4.02
1728 1936 0.473755 TGCTCTGCCTTTCTGTCCAA 59.526 50.000 0.00 0.00 0.00 3.53
1840 2050 5.535406 TCAGGGGTTTTCTTGCGTATTTTTA 59.465 36.000 0.00 0.00 0.00 1.52
1897 2107 9.545105 AAATCATAATGCTGAAACTTTTTGTGA 57.455 25.926 0.00 0.00 0.00 3.58
2159 2377 3.691342 CCGCTGGGGACTCGAACA 61.691 66.667 4.46 0.00 38.47 3.18
2221 2439 0.107456 CCGCTAGGACAGATGGCAAT 59.893 55.000 0.00 0.00 41.02 3.56
2323 2553 3.074594 ACGCGTGAGAGTGGTTTTT 57.925 47.368 12.93 0.00 44.38 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.364186 GGGGCTTTGTGATGGGGG 60.364 66.667 0.00 0.00 0.00 5.40
21 22 0.261402 TATGGGGCTTTGTGATGGGG 59.739 55.000 0.00 0.00 0.00 4.96
26 27 2.530460 AGCAATATGGGGCTTTGTGA 57.470 45.000 0.00 0.00 36.92 3.58
67 69 5.128919 GTGACCATGGAGCTTTGAGAATAT 58.871 41.667 21.47 0.00 0.00 1.28
69 71 3.350833 GTGACCATGGAGCTTTGAGAAT 58.649 45.455 21.47 0.00 0.00 2.40
115 117 8.712228 TTGATAGAGGAGCATAGACAATTAGA 57.288 34.615 0.00 0.00 0.00 2.10
116 118 8.801299 TCTTGATAGAGGAGCATAGACAATTAG 58.199 37.037 0.00 0.00 0.00 1.73
117 119 8.712228 TCTTGATAGAGGAGCATAGACAATTA 57.288 34.615 0.00 0.00 0.00 1.40
118 120 7.609097 TCTTGATAGAGGAGCATAGACAATT 57.391 36.000 0.00 0.00 0.00 2.32
119 121 7.454066 TCATCTTGATAGAGGAGCATAGACAAT 59.546 37.037 0.00 0.00 36.36 2.71
120 122 6.779539 TCATCTTGATAGAGGAGCATAGACAA 59.220 38.462 0.00 0.00 36.36 3.18
121 123 6.310149 TCATCTTGATAGAGGAGCATAGACA 58.690 40.000 0.00 0.00 36.36 3.41
122 124 6.832520 TCATCTTGATAGAGGAGCATAGAC 57.167 41.667 0.00 0.00 36.36 2.59
123 125 7.559533 GGTATCATCTTGATAGAGGAGCATAGA 59.440 40.741 0.00 0.00 43.70 1.98
185 187 4.495844 GCAAAACAAGTCACTGTACTCCAC 60.496 45.833 0.00 0.00 0.00 4.02
202 204 2.233186 ACTCTACTCCTACCCGCAAAAC 59.767 50.000 0.00 0.00 0.00 2.43
220 222 8.764524 AAGTCATTACTATGTCAAAGTCACTC 57.235 34.615 0.00 0.00 33.75 3.51
246 248 4.931601 TCATTCTCAGTTTCCTCACATTCG 59.068 41.667 0.00 0.00 0.00 3.34
247 249 6.169094 TCTCATTCTCAGTTTCCTCACATTC 58.831 40.000 0.00 0.00 0.00 2.67
260 262 3.030873 ACCCCTCTCTCTCATTCTCAG 57.969 52.381 0.00 0.00 0.00 3.35
284 288 5.399596 GTCTGCATATATACATACGGATGCG 59.600 44.000 7.78 4.58 42.00 4.73
286 290 7.976175 ACTTGTCTGCATATATACATACGGATG 59.024 37.037 5.94 5.94 39.16 3.51
290 294 6.586082 TGCACTTGTCTGCATATATACATACG 59.414 38.462 0.00 0.00 42.36 3.06
318 322 1.538047 TGCTCTTTTCATGAGGCACC 58.462 50.000 0.00 0.00 32.57 5.01
356 360 1.846007 TGTGTGGGTGCTCACTTTTT 58.154 45.000 3.72 0.00 38.40 1.94
357 361 1.846007 TTGTGTGGGTGCTCACTTTT 58.154 45.000 3.72 0.00 38.40 2.27
358 362 1.846007 TTTGTGTGGGTGCTCACTTT 58.154 45.000 3.72 0.00 38.40 2.66
359 363 1.476488 GTTTTGTGTGGGTGCTCACTT 59.524 47.619 3.72 0.00 38.40 3.16
360 364 1.102978 GTTTTGTGTGGGTGCTCACT 58.897 50.000 3.72 0.00 38.40 3.41
361 365 0.814457 TGTTTTGTGTGGGTGCTCAC 59.186 50.000 0.00 0.00 38.09 3.51
362 366 1.476085 CTTGTTTTGTGTGGGTGCTCA 59.524 47.619 0.00 0.00 0.00 4.26
363 367 1.476488 ACTTGTTTTGTGTGGGTGCTC 59.524 47.619 0.00 0.00 0.00 4.26
364 368 1.204467 CACTTGTTTTGTGTGGGTGCT 59.796 47.619 0.00 0.00 0.00 4.40
365 369 1.067213 ACACTTGTTTTGTGTGGGTGC 60.067 47.619 0.00 0.00 45.57 5.01
366 370 3.733684 GCTACACTTGTTTTGTGTGGGTG 60.734 47.826 9.42 0.00 46.54 4.61
367 371 2.425668 GCTACACTTGTTTTGTGTGGGT 59.574 45.455 9.42 0.00 46.54 4.51
368 372 2.425312 TGCTACACTTGTTTTGTGTGGG 59.575 45.455 9.42 4.29 46.54 4.61
369 373 3.773860 TGCTACACTTGTTTTGTGTGG 57.226 42.857 9.42 7.71 46.54 4.17
370 374 3.486841 GCATGCTACACTTGTTTTGTGTG 59.513 43.478 11.37 0.00 46.54 3.82
372 376 2.720578 CGCATGCTACACTTGTTTTGTG 59.279 45.455 17.13 0.00 40.87 3.33
373 377 2.357637 ACGCATGCTACACTTGTTTTGT 59.642 40.909 17.13 0.00 0.00 2.83
374 378 2.973224 GACGCATGCTACACTTGTTTTG 59.027 45.455 17.13 0.00 0.00 2.44
375 379 2.031157 GGACGCATGCTACACTTGTTTT 60.031 45.455 17.13 0.00 0.00 2.43
376 380 1.535462 GGACGCATGCTACACTTGTTT 59.465 47.619 17.13 0.00 0.00 2.83
377 381 1.156736 GGACGCATGCTACACTTGTT 58.843 50.000 17.13 0.00 0.00 2.83
378 382 0.321671 AGGACGCATGCTACACTTGT 59.678 50.000 17.13 3.76 0.00 3.16
379 383 1.002366 GAGGACGCATGCTACACTTG 58.998 55.000 17.13 0.00 0.00 3.16
380 384 0.608130 TGAGGACGCATGCTACACTT 59.392 50.000 17.13 0.45 0.00 3.16
381 385 0.826715 ATGAGGACGCATGCTACACT 59.173 50.000 17.13 8.40 0.00 3.55
382 386 0.933097 CATGAGGACGCATGCTACAC 59.067 55.000 17.13 4.98 39.19 2.90
383 387 0.823460 TCATGAGGACGCATGCTACA 59.177 50.000 17.13 8.64 44.08 2.74
384 388 1.939974 TTCATGAGGACGCATGCTAC 58.060 50.000 17.13 9.21 44.08 3.58
385 389 2.279741 GTTTCATGAGGACGCATGCTA 58.720 47.619 17.13 0.16 44.08 3.49
386 390 1.089920 GTTTCATGAGGACGCATGCT 58.910 50.000 17.13 2.38 44.08 3.79
387 391 0.099436 GGTTTCATGAGGACGCATGC 59.901 55.000 7.91 7.91 44.08 4.06
388 392 1.452110 TGGTTTCATGAGGACGCATG 58.548 50.000 9.37 9.37 45.41 4.06
389 393 2.086869 CTTGGTTTCATGAGGACGCAT 58.913 47.619 0.00 0.00 0.00 4.73
390 394 1.202758 ACTTGGTTTCATGAGGACGCA 60.203 47.619 0.00 0.00 0.00 5.24
391 395 1.523758 ACTTGGTTTCATGAGGACGC 58.476 50.000 0.00 0.00 0.00 5.19
392 396 5.631026 CATTAACTTGGTTTCATGAGGACG 58.369 41.667 0.00 0.00 0.00 4.79
393 397 5.048083 TGCATTAACTTGGTTTCATGAGGAC 60.048 40.000 0.00 0.00 0.00 3.85
394 398 5.076182 TGCATTAACTTGGTTTCATGAGGA 58.924 37.500 0.00 0.00 0.00 3.71
395 399 5.389859 TGCATTAACTTGGTTTCATGAGG 57.610 39.130 0.00 0.00 0.00 3.86
396 400 8.984891 TTTATGCATTAACTTGGTTTCATGAG 57.015 30.769 3.54 0.00 0.00 2.90
397 401 9.941325 ATTTTATGCATTAACTTGGTTTCATGA 57.059 25.926 3.54 0.00 0.00 3.07
400 404 9.421806 CAGATTTTATGCATTAACTTGGTTTCA 57.578 29.630 3.54 0.00 0.00 2.69
401 405 8.872845 CCAGATTTTATGCATTAACTTGGTTTC 58.127 33.333 3.54 0.00 0.00 2.78
402 406 7.823799 CCCAGATTTTATGCATTAACTTGGTTT 59.176 33.333 3.54 0.00 0.00 3.27
403 407 7.180051 TCCCAGATTTTATGCATTAACTTGGTT 59.820 33.333 3.54 0.00 0.00 3.67
404 408 6.667414 TCCCAGATTTTATGCATTAACTTGGT 59.333 34.615 3.54 0.00 0.00 3.67
405 409 6.980397 GTCCCAGATTTTATGCATTAACTTGG 59.020 38.462 3.54 9.43 0.00 3.61
406 410 7.775120 AGTCCCAGATTTTATGCATTAACTTG 58.225 34.615 3.54 0.53 0.00 3.16
407 411 7.961326 AGTCCCAGATTTTATGCATTAACTT 57.039 32.000 3.54 0.00 0.00 2.66
408 412 7.961326 AAGTCCCAGATTTTATGCATTAACT 57.039 32.000 3.54 0.00 0.00 2.24
409 413 8.470002 AGAAAGTCCCAGATTTTATGCATTAAC 58.530 33.333 3.54 0.00 0.00 2.01
410 414 8.593945 AGAAAGTCCCAGATTTTATGCATTAA 57.406 30.769 3.54 0.00 0.00 1.40
411 415 9.866655 ATAGAAAGTCCCAGATTTTATGCATTA 57.133 29.630 3.54 0.00 0.00 1.90
412 416 8.636213 CATAGAAAGTCCCAGATTTTATGCATT 58.364 33.333 3.54 0.00 0.00 3.56
413 417 7.255730 GCATAGAAAGTCCCAGATTTTATGCAT 60.256 37.037 3.79 3.79 36.59 3.96
414 418 6.039717 GCATAGAAAGTCCCAGATTTTATGCA 59.960 38.462 12.55 0.00 36.59 3.96
415 419 6.442112 GCATAGAAAGTCCCAGATTTTATGC 58.558 40.000 5.04 5.04 33.55 3.14
416 420 6.774656 AGGCATAGAAAGTCCCAGATTTTATG 59.225 38.462 0.00 0.00 0.00 1.90
417 421 6.915786 AGGCATAGAAAGTCCCAGATTTTAT 58.084 36.000 0.00 0.00 0.00 1.40
418 422 6.327386 AGGCATAGAAAGTCCCAGATTTTA 57.673 37.500 0.00 0.00 0.00 1.52
419 423 5.198602 AGGCATAGAAAGTCCCAGATTTT 57.801 39.130 0.00 0.00 0.00 1.82
420 424 4.870021 AGGCATAGAAAGTCCCAGATTT 57.130 40.909 0.00 0.00 0.00 2.17
421 425 4.228210 TCAAGGCATAGAAAGTCCCAGATT 59.772 41.667 0.00 0.00 0.00 2.40
422 426 3.782523 TCAAGGCATAGAAAGTCCCAGAT 59.217 43.478 0.00 0.00 0.00 2.90
423 427 3.055094 GTCAAGGCATAGAAAGTCCCAGA 60.055 47.826 0.00 0.00 0.00 3.86
424 428 3.274288 GTCAAGGCATAGAAAGTCCCAG 58.726 50.000 0.00 0.00 0.00 4.45
425 429 2.642311 TGTCAAGGCATAGAAAGTCCCA 59.358 45.455 0.00 0.00 0.00 4.37
426 430 3.274288 CTGTCAAGGCATAGAAAGTCCC 58.726 50.000 0.00 0.00 0.00 4.46
427 431 3.055094 TCCTGTCAAGGCATAGAAAGTCC 60.055 47.826 0.00 0.00 44.11 3.85
428 432 4.081420 TCTCCTGTCAAGGCATAGAAAGTC 60.081 45.833 0.00 0.00 44.11 3.01
429 433 3.840666 TCTCCTGTCAAGGCATAGAAAGT 59.159 43.478 0.00 0.00 44.11 2.66
430 434 4.478206 TCTCCTGTCAAGGCATAGAAAG 57.522 45.455 0.00 0.00 44.11 2.62
431 435 4.384537 CCATCTCCTGTCAAGGCATAGAAA 60.385 45.833 0.00 0.00 44.11 2.52
432 436 3.135348 CCATCTCCTGTCAAGGCATAGAA 59.865 47.826 0.00 0.00 44.11 2.10
433 437 2.702478 CCATCTCCTGTCAAGGCATAGA 59.298 50.000 0.00 0.00 44.11 1.98
434 438 2.702478 TCCATCTCCTGTCAAGGCATAG 59.298 50.000 0.00 0.00 44.11 2.23
435 439 2.702478 CTCCATCTCCTGTCAAGGCATA 59.298 50.000 0.00 0.00 44.11 3.14
436 440 1.489649 CTCCATCTCCTGTCAAGGCAT 59.510 52.381 0.00 0.00 44.11 4.40
437 441 0.907486 CTCCATCTCCTGTCAAGGCA 59.093 55.000 0.00 0.00 44.11 4.75
438 442 0.908198 ACTCCATCTCCTGTCAAGGC 59.092 55.000 0.00 0.00 44.11 4.35
439 443 2.568956 TGAACTCCATCTCCTGTCAAGG 59.431 50.000 0.00 0.00 46.06 3.61
440 444 3.007290 TGTGAACTCCATCTCCTGTCAAG 59.993 47.826 0.00 0.00 0.00 3.02
441 445 2.972021 TGTGAACTCCATCTCCTGTCAA 59.028 45.455 0.00 0.00 0.00 3.18
442 446 2.300152 GTGTGAACTCCATCTCCTGTCA 59.700 50.000 0.00 0.00 0.00 3.58
443 447 2.300152 TGTGTGAACTCCATCTCCTGTC 59.700 50.000 0.00 0.00 0.00 3.51
444 448 2.037772 GTGTGTGAACTCCATCTCCTGT 59.962 50.000 0.00 0.00 0.00 4.00
445 449 2.037641 TGTGTGTGAACTCCATCTCCTG 59.962 50.000 0.00 0.00 0.00 3.86
446 450 2.329267 TGTGTGTGAACTCCATCTCCT 58.671 47.619 0.00 0.00 0.00 3.69
447 451 2.839486 TGTGTGTGAACTCCATCTCC 57.161 50.000 0.00 0.00 0.00 3.71
448 452 3.438087 CCATTGTGTGTGAACTCCATCTC 59.562 47.826 0.00 0.00 0.00 2.75
449 453 3.415212 CCATTGTGTGTGAACTCCATCT 58.585 45.455 0.00 0.00 0.00 2.90
450 454 2.489329 CCCATTGTGTGTGAACTCCATC 59.511 50.000 0.00 0.00 0.00 3.51
451 455 2.108075 TCCCATTGTGTGTGAACTCCAT 59.892 45.455 0.00 0.00 0.00 3.41
452 456 1.492599 TCCCATTGTGTGTGAACTCCA 59.507 47.619 0.00 0.00 0.00 3.86
453 457 2.270352 TCCCATTGTGTGTGAACTCC 57.730 50.000 0.00 0.00 0.00 3.85
454 458 3.550842 GCTTTCCCATTGTGTGTGAACTC 60.551 47.826 0.00 0.00 0.00 3.01
455 459 2.362077 GCTTTCCCATTGTGTGTGAACT 59.638 45.455 0.00 0.00 0.00 3.01
456 460 2.742774 GCTTTCCCATTGTGTGTGAAC 58.257 47.619 0.00 0.00 0.00 3.18
457 461 1.336440 CGCTTTCCCATTGTGTGTGAA 59.664 47.619 0.00 0.00 0.00 3.18
458 462 0.950836 CGCTTTCCCATTGTGTGTGA 59.049 50.000 0.00 0.00 0.00 3.58
459 463 0.667993 ACGCTTTCCCATTGTGTGTG 59.332 50.000 0.00 0.00 0.00 3.82
460 464 2.264005 TACGCTTTCCCATTGTGTGT 57.736 45.000 0.00 0.00 0.00 3.72
461 465 2.552315 AGTTACGCTTTCCCATTGTGTG 59.448 45.455 0.00 0.00 0.00 3.82
462 466 2.858745 AGTTACGCTTTCCCATTGTGT 58.141 42.857 0.00 0.00 0.00 3.72
463 467 3.252215 TGAAGTTACGCTTTCCCATTGTG 59.748 43.478 0.00 0.00 37.59 3.33
464 468 3.482436 TGAAGTTACGCTTTCCCATTGT 58.518 40.909 0.00 0.00 37.59 2.71
465 469 3.502211 ACTGAAGTTACGCTTTCCCATTG 59.498 43.478 0.00 0.00 37.59 2.82
466 470 3.751518 ACTGAAGTTACGCTTTCCCATT 58.248 40.909 0.00 0.00 37.59 3.16
467 471 3.418684 ACTGAAGTTACGCTTTCCCAT 57.581 42.857 0.00 0.00 37.59 4.00
468 472 2.922740 ACTGAAGTTACGCTTTCCCA 57.077 45.000 0.00 0.00 37.59 4.37
469 473 3.434641 GGTTACTGAAGTTACGCTTTCCC 59.565 47.826 0.00 0.00 37.59 3.97
470 474 3.122445 CGGTTACTGAAGTTACGCTTTCC 59.878 47.826 0.00 0.00 37.59 3.13
471 475 3.983344 TCGGTTACTGAAGTTACGCTTTC 59.017 43.478 0.00 0.00 37.59 2.62
472 476 3.981211 TCGGTTACTGAAGTTACGCTTT 58.019 40.909 0.00 0.00 37.59 3.51
473 477 3.648339 TCGGTTACTGAAGTTACGCTT 57.352 42.857 0.00 0.00 40.76 4.68
474 478 3.243501 TGTTCGGTTACTGAAGTTACGCT 60.244 43.478 6.89 0.00 0.00 5.07
475 479 3.052036 TGTTCGGTTACTGAAGTTACGC 58.948 45.455 6.89 0.00 0.00 4.42
476 480 4.433805 GCATGTTCGGTTACTGAAGTTACG 60.434 45.833 6.89 0.00 0.00 3.18
477 481 4.449743 TGCATGTTCGGTTACTGAAGTTAC 59.550 41.667 6.89 0.00 0.00 2.50
478 482 4.633175 TGCATGTTCGGTTACTGAAGTTA 58.367 39.130 6.89 0.00 0.00 2.24
479 483 3.472652 TGCATGTTCGGTTACTGAAGTT 58.527 40.909 6.89 0.00 0.00 2.66
480 484 3.067106 CTGCATGTTCGGTTACTGAAGT 58.933 45.455 6.89 0.00 0.00 3.01
481 485 3.067106 ACTGCATGTTCGGTTACTGAAG 58.933 45.455 6.89 0.00 0.00 3.02
482 486 3.120321 ACTGCATGTTCGGTTACTGAA 57.880 42.857 2.02 2.02 0.00 3.02
483 487 2.831685 ACTGCATGTTCGGTTACTGA 57.168 45.000 0.00 0.00 0.00 3.41
484 488 3.322369 TGTACTGCATGTTCGGTTACTG 58.678 45.455 0.00 0.00 0.00 2.74
485 489 3.671008 TGTACTGCATGTTCGGTTACT 57.329 42.857 0.00 0.00 0.00 2.24
486 490 4.735662 TTTGTACTGCATGTTCGGTTAC 57.264 40.909 0.00 0.00 0.00 2.50
487 491 7.618502 ATTATTTGTACTGCATGTTCGGTTA 57.381 32.000 0.00 0.00 0.00 2.85
488 492 5.950758 TTATTTGTACTGCATGTTCGGTT 57.049 34.783 0.00 0.00 0.00 4.44
489 493 6.150307 TGAATTATTTGTACTGCATGTTCGGT 59.850 34.615 0.00 0.00 0.00 4.69
490 494 6.550843 TGAATTATTTGTACTGCATGTTCGG 58.449 36.000 0.00 0.00 0.00 4.30
491 495 8.619146 ATTGAATTATTTGTACTGCATGTTCG 57.381 30.769 0.00 0.00 0.00 3.95
497 501 9.518906 CAGCATAATTGAATTATTTGTACTGCA 57.481 29.630 15.51 0.00 33.34 4.41
498 502 8.971321 CCAGCATAATTGAATTATTTGTACTGC 58.029 33.333 7.66 8.17 33.34 4.40
499 503 8.971321 GCCAGCATAATTGAATTATTTGTACTG 58.029 33.333 7.66 9.84 33.34 2.74
500 504 8.694540 TGCCAGCATAATTGAATTATTTGTACT 58.305 29.630 7.66 0.00 33.34 2.73
501 505 8.870160 TGCCAGCATAATTGAATTATTTGTAC 57.130 30.769 7.66 5.54 33.34 2.90
502 506 8.143193 CCTGCCAGCATAATTGAATTATTTGTA 58.857 33.333 7.66 2.21 33.34 2.41
503 507 6.987992 CCTGCCAGCATAATTGAATTATTTGT 59.012 34.615 7.66 0.00 33.34 2.83
504 508 6.987992 ACCTGCCAGCATAATTGAATTATTTG 59.012 34.615 7.66 9.17 33.34 2.32
505 509 6.987992 CACCTGCCAGCATAATTGAATTATTT 59.012 34.615 7.66 0.00 33.34 1.40
506 510 6.518493 CACCTGCCAGCATAATTGAATTATT 58.482 36.000 7.66 0.00 33.34 1.40
507 511 5.510179 GCACCTGCCAGCATAATTGAATTAT 60.510 40.000 4.65 4.65 33.76 1.28
508 512 4.202141 GCACCTGCCAGCATAATTGAATTA 60.202 41.667 0.00 0.00 34.31 1.40
509 513 3.431207 GCACCTGCCAGCATAATTGAATT 60.431 43.478 0.00 0.00 34.31 2.17
510 514 2.101917 GCACCTGCCAGCATAATTGAAT 59.898 45.455 0.00 0.00 34.31 2.57
511 515 1.477700 GCACCTGCCAGCATAATTGAA 59.522 47.619 0.00 0.00 34.31 2.69
512 516 1.105457 GCACCTGCCAGCATAATTGA 58.895 50.000 0.00 0.00 34.31 2.57
513 517 0.818938 TGCACCTGCCAGCATAATTG 59.181 50.000 0.00 0.00 41.18 2.32
514 518 3.286404 TGCACCTGCCAGCATAATT 57.714 47.368 0.00 0.00 41.18 1.40
519 523 2.986979 CACATGCACCTGCCAGCA 60.987 61.111 0.00 0.00 45.92 4.41
520 524 4.430765 GCACATGCACCTGCCAGC 62.431 66.667 6.20 0.00 41.18 4.85
528 532 1.669999 GATTCCCAGGGCACATGCAC 61.670 60.000 0.00 1.17 46.94 4.57
529 533 1.380246 GATTCCCAGGGCACATGCA 60.380 57.895 0.00 0.00 44.36 3.96
530 534 1.380246 TGATTCCCAGGGCACATGC 60.380 57.895 0.00 0.00 41.14 4.06
531 535 0.323633 TGTGATTCCCAGGGCACATG 60.324 55.000 12.26 0.00 36.44 3.21
532 536 0.632835 ATGTGATTCCCAGGGCACAT 59.367 50.000 19.63 19.63 44.15 3.21
533 537 1.212688 CTATGTGATTCCCAGGGCACA 59.787 52.381 17.21 17.21 44.31 4.57
534 538 1.477558 CCTATGTGATTCCCAGGGCAC 60.478 57.143 0.00 3.99 0.00 5.01
535 539 0.846015 CCTATGTGATTCCCAGGGCA 59.154 55.000 0.00 0.00 0.00 5.36
536 540 0.846693 ACCTATGTGATTCCCAGGGC 59.153 55.000 0.00 0.00 0.00 5.19
537 541 1.143684 CCACCTATGTGATTCCCAGGG 59.856 57.143 0.00 0.00 45.76 4.45
538 542 1.477558 GCCACCTATGTGATTCCCAGG 60.478 57.143 0.00 0.00 45.76 4.45
539 543 1.212688 TGCCACCTATGTGATTCCCAG 59.787 52.381 0.00 0.00 45.76 4.45
540 544 1.294041 TGCCACCTATGTGATTCCCA 58.706 50.000 0.00 0.00 45.76 4.37
541 545 2.233271 CATGCCACCTATGTGATTCCC 58.767 52.381 0.00 0.00 45.76 3.97
542 546 2.936202 ACATGCCACCTATGTGATTCC 58.064 47.619 0.00 0.00 45.76 3.01
543 547 5.618056 CATACATGCCACCTATGTGATTC 57.382 43.478 0.00 0.00 45.76 2.52
558 562 9.906660 ATTAACCCATTTATAAACGCATACATG 57.093 29.630 0.00 0.00 0.00 3.21
564 568 9.357161 AGGATAATTAACCCATTTATAAACGCA 57.643 29.630 8.09 0.00 0.00 5.24
625 629 1.065926 AGCACAATTCGCATCTGAGGA 60.066 47.619 0.00 0.00 0.00 3.71
787 796 0.759346 AACGACTCTTTGCTGGGTCT 59.241 50.000 0.00 0.00 0.00 3.85
802 811 0.952280 AACGACTCTCTGCTCAACGA 59.048 50.000 0.00 0.00 0.00 3.85
1090 1103 1.002087 AGAAACCCTTCGATCAACGCT 59.998 47.619 0.00 0.00 42.26 5.07
1175 1221 3.305110 GACGACGAAAATGGTGCAATTT 58.695 40.909 0.00 0.00 0.00 1.82
1202 1390 3.030291 TCACCTGCATGAACTTGGTTTT 58.970 40.909 0.00 0.00 0.00 2.43
1408 1616 4.974645 TCAAGCTTCCTAACCTTCTTCA 57.025 40.909 0.00 0.00 0.00 3.02
1897 2107 7.342799 TGGCTCTGGAATAATTCAATTAGCTTT 59.657 33.333 0.00 0.00 0.00 3.51
1917 2127 7.833285 TTTCTAACCTTAATTGTTTGGCTCT 57.167 32.000 0.00 0.00 0.00 4.09
2143 2361 2.432628 GTGTTCGAGTCCCCAGCG 60.433 66.667 0.00 0.00 0.00 5.18
2173 2391 1.410882 GCAGCCCTAAACACCACAAAA 59.589 47.619 0.00 0.00 0.00 2.44
2221 2439 3.521937 CCTTCCCTACCCATGTCAAAGTA 59.478 47.826 0.00 0.00 0.00 2.24
2295 2525 1.061729 CTCACGCGTGTGCAAACAA 59.938 52.632 35.74 15.39 46.01 2.83
2347 2577 4.037222 ACATTTTCAACCTTCCAACCCTT 58.963 39.130 0.00 0.00 0.00 3.95


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.